segunda-feira, junho 29, 2015

The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

David Roy Smith

David Roy Smith is an assistant professor of biology at the University of Western Ontario, where he studies genome evolution of eukaryotic microbes. He can be found online at www.arrogantgenome.com and @arrogantgenome.

The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank—an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Galápagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Galápagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms.

segunda-feira, junho 22, 2015

The "Random Genetic Drift" Fallacy Paperback – September 10, 2014

by Prof William B. Provine (Author)

Much of my life has been devoted to the history of population genetics. My early book was my Ph.D. thesis still in print: The Origins of Theoretical Populations Genetics (1971, 2nd edition, 1991). I stated in the 2nd edition in the Afterword that “random genetic drift” was giving me pause, as does the evolutionary synthesis. My later book was Sewall Wright and Evolutionary Biology (1986) and is also still in print. Now I am writing this book against “random genetic drift,” invented by R. A. Fisher and followed by Sewall Wright and J. B. S. Haldane. “Random genetic drift” is the core of population genetics. Any person who believes in “random genetic drift” should read this book.

The oft-repeated claim that Earth’s biota is entering a sixth “mass extinction” depends on clearly demonstrating that current extinction rates are far above the “background” rates prevailing in the five previous mass extinctions. Earlier estimates of extinction rates have been criticized for using assumptions that might overestimate the severity of the extinction crisis. We assess, using extremely conservative assumptions, whether human activities are causing a mass extinction. First, we use a recent estimate of a background rate of 2 mammal extinctions per 10,000 species per 100 years (that is, 2 E/MSY), which is twice as high as widely used previous estimates. We then compare this rate with the current rate of mammal and vertebrate extinctions. The latter is conservatively low because listing a species as extinct requires meeting stringent criteria. Even under our assumptions, which would tend to minimize evidence of an incipient mass extinction, the average rate of vertebrate species loss over the last century is up to 114 times higher than the background rate. Under the 2 E/MSY background rate, the number of species that have gone extinct in the last century would have taken, depending on the vertebrate taxon, between 800 and 10,000 years to disappear. These estimates reveal an exceptionally rapid loss of biodiversity over the last few centuries, indicating that a sixth mass extinction is already under way. Averting a dramatic decay of biodiversity and the subsequent loss of ecosystem services is still possible through intensified conservation efforts, but that window of opportunity is rapidly closing.

Inside the head of the worm C. elegans, the TV antenna-like structure at the tip of the AFD neuron (green) is the first identified sensor for Earth's magnetic field. Credit: Andres Vidal-Gadea.

ABSTRACT

Many organisms spanning from bacteria to mammals orient to the earth's magnetic field. For a few animals, central neurons responsive to earth-strength magnetic fields have been identified; however, magnetosensory neurons have yet to be identified in any animal. We show that the nematode Caenorhabditis elegans orients to the earth's magnetic field during vertical burrowing migrations. Well-fed worms migrated up, while starved worms migrated down. Populations isolated from around the world, migrated at angles to the magnetic vector that would optimize vertical translation in their native soil, with northern- and southern-hemisphere worms displaying opposite migratory preferences. Magnetic orientation and vertical migrations required the TAX-4 cyclic nucleotide-gated ion channel in the AFD sensory neuron pair. Calcium imaging showed that these neurons respond to magnetic fields even without synaptic input. C. elegans may have adapted magnetic orientation to simplify their vertical burrowing migration by reducing the orientation task from three dimensions to one.

The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease.Nevertheless, our current estimates of the rate are uncertain. Classical methods based on sequence divergence have yielded significantly larger values than more recent approaches based on counting de novo mutations in family pedigrees. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.65 +/- 0.10 x 10^(-8) mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.

Copyright

The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver

Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental concepts, including the question of ‘what is life?’. To re-energize the research and define a new experimental paradigm, we advance four premises to better understand the physicochemical complexities of life’s emergence:

(1) Chemical and Darwinian (biological) evolutions are distinct, but become continuous with the appearance of heredity.

(2) Earth’s chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal vents.

(3) Earth’s overall chemical complexity must be high at the origin of life for a subset of (complex) chemicals to phase separate and evolve into living states.

We discuss these premises in relation to current ‘constructive’ (non-evolutionary) paradigm of origins research – the process of complexification of chemical matter ‘from the simple to the complex’. This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics. Our four premises suggest an empirical program of experiments involving complex chemical compositions under cycling gradients of temperature, water activity and electromagnetic radiation.

Received 25 January 2015 Accepted 30 April 2015 Published 09 June 2015

Abstract

Abstract• References• Author information• Supplementary information

Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ~67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals.

It is not really helpful to consider modern environmental epigenetics as neo-Lamarckian; and there is no evidence that Lamarck considered the idea original to himself. We must all keep learning about inheritance, but attributing modern ideas to early researchers is not helpful, and can be misleading.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

• Some demethylation resistant loci are candidates for epigenetic inheritance

Summary

Resetting of the epigenome in human primordial germ cells (hPGCs) is critical for development. We show that the transcriptional program of hPGCs is distinct from that in mice, with co-expression of somatic specifiers and naive pluripotency genes TFCP2L1 and KLF4. This unique gene regulatory network, established by SOX17 and BLIMP1, drives comprehensive germline DNA demethylation by repressing DNA methylation pathways and activating TET-mediated hydroxymethylation. Base-resolution methylome analysis reveals progressive DNA demethylation to basal levels in week 5–7 in vivo hPGCs. Concurrently, hPGCs undergo chromatin reorganization, X reactivation, and imprint erasure. Despite global hypomethylation, evolutionarily young and potentially hazardous retroelements, like SVA, remain methylated. Remarkably, some loci associated with metabolic and neurological disorders are also resistant to DNA demethylation, revealing potential for transgenerational epigenetic inheritance that may have phenotypic consequences. We provide comprehensive insight on early human germline transcriptional network and epigenetic reprogramming that subsequently impacts human development and disease.

It is generally assumed that mRNAs undergoing translation are protected from decay. Here, we show that mRNAs are, in fact, co-translationally degraded. This is a widespread and conserved process affecting most genes, where 5′–3′ transcript degradation follows the last translating ribosome, producing an in vivo ribosomal footprint. By sequencing the ends of 5′ phosphorylated mRNA degradation intermediates, we obtain a genome-wide drug-free measurement of ribosome dynamics. We identify general translation termination pauses in both normal and stress conditions. In addition, we describe novel codon-specific ribosomal pausing sites in response to oxidative stress that are dependent on the RNase Rny1. Our approach is simple and straightforward and does not require the use of translational inhibitors or in vitro RNA footprinting that can alter ribosome protection patterns.

The advent of oxygenic photosynthesis set the stage for the evolution of complex life on an oxygenated planet, but it is unknown when this transformative biochemistry emerged. The existing hydrocarbon biomarker record requires that oxygenic photosynthesis and eukaryotes emerged more than 300 million years before the Great Oxidation Event [∼2.4 billion years ago (Ga)]. We report that hopane and sterane concentrations measured in new ultraclean Archean drill cores from Australia are comparable to blank concentrations, yet their concentrations in the exteriors of conventionally collected cores of stratigraphic equivalence exceed blank concentrations by more than an order of magnitude due to surficial contamination. Consequently, previous hydrocarbon biomarker reports no longer provide valid evidence for the advent of oxygenic photosynthesis and eukaryotes by ∼2.7 Ga.

Abstract

Hopanes and steranes found in Archean rocks have been presented as key evidence supporting the early rise of oxygenic photosynthesis and eukaryotes, but the syngeneity of these hydrocarbon biomarkers is controversial. To resolve this debate, we performed a multilaboratory study of new cores from the Pilbara Craton, Australia, that were drilled and sampled using unprecedented hydrocarbon-clean protocols. Hopanes and steranes in rock extracts and hydropyrolysates from these new cores were typically at or below our femtogram detection limit, but when they were detectable, they had total hopane < 37.9 pg per gram of rock > and total sterane < 32.9 pg per gram of rock > concentrations comparable to those measured in blanks and negative control samples. In contrast, hopanes and steranes measured in the exteriors of conventionally drilled and curated rocks of stratigraphic equivalence reach concentrations of 389.5 pg per gram of rock and 1,039 pg per gram of rock, respectively. Polycyclic aromatic hydrocarbons and diamondoids, which exceed blank concentrations, exhibit individual concentrations up to 80 ng per gram of rock in rock extracts and up to 1,000 ng per gram of rock in hydropyrolysates from the ultraclean cores.These results demonstrate that previously studied Archean samples host mixtures of biomarker contaminants and indigenous overmature hydrocarbons.

Therefore, existing lipid biomarker evidence cannot be invoked to support the emergence of oxygenic photosynthesis and eukaryotes by ∼2.7 billion years ago.Although suitable Proterozoic rocks exist, no currently known Archean strata lie within the appropriate thermal maturity window for syngenetic hydrocarbon biomarker preservation, so future exploration for Archean biomarkers should screen for rocks with milder thermal histories.

RNA editing by adenosine deamination alters genetic information from the genomic blueprint. When it recodes mRNAs, it gives organisms the option to express diverse, functionally distinct, protein isoforms. All eumetazoans, from cnidarians to humans, express RNA editing enzymes. However, transcriptome-wide screens have only uncovered about 25 transcripts harboring conserved recoding RNA editing sites in mammals and several hundred recoding sites in Drosophila. These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare. Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent. We identify 57,108 recoding sites in the nervous system, affecting the majority of the proteins studied. Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.

DOI: http://dx.doi.org/10.7554/eLife.05198.001

Excerpt/Excerto:

Introduction

The central dogma of biology maintains that genetic information passes faithfully from DNA to RNA to proteins;however, with the help of tools such as alternative splicing, organisms use RNA as a canvas to modify and enrich this flow of information.RNA editing by deamination of adenosine to inosine (A-to-I) is another process used to alter genetic information (Nishikura, 2010). Unlike alternative splicing, which shuffles relatively large regions of RNA, editing targets single bases in order to fine-tune protein function. Because inosine is interpreted as guanosine by the cellular machinery, this process can recode codons (Basilio et al., 1962). A-to-I RNA editing is catalyzed by the ADAR (adenosine deaminase that acts on RNA) family of enzymes. All eumetazoans, from cnidarians to mammals, express ADARs but the extent to which they use them to recode has been explored in few representatives (Nishikura, 2010).

Recent advances in DNA sequencing and the supporting computational analyses have permitted transcriptome-wide screens for RNA editing events. So far, such studies have been limited to organisms with a sequenced genome (Ramaswami et al., 2012, 2013). In general, these screens have looked for variation in RNA at positions that are invariant in the genome. In humans, inosine is abundant in RNA (Paul and Bass, 1998; Bazak et al., 2014), but almost all of it lies within transcribed repetitive elements in untranslated regions or introns (Nishikura, 2010). A compilation of recoding sites in human transcriptomes revealed 1183 events (Xu and Zhang, 2014), but most were observed in only a single sample. Individual searches (Danecek et al., 2012; Ramaswami et al., 2013) uncovered only 115 (non-repetitive) recoding events, and 53 in mice; 34 recoding sites are conserved across mammals (Pinto et al., 2014). In Drosophila, an order of magnitude more recoding sites have been identified, residing in about 3% of all messages (St Laurent et al., 2013). Although individual editing sites are clearly essential (Brusa et al., 1995), these data suggest that RNA editing is not a broadly used mechanism for proteome diversification.

However, anecdotal data suggest this assumption might not apply across the animal kingdom. For example, using traditional cloning methods, scores of recoding sites have been uncovered in a small number of squid and octopus transcripts encoding potassium channels, ADARs, and ion pumps (Garrett and Rosenthal, 2012a). As for most organisms, there are no genomes available for cephalopods. Here we apply a novel approach for editing site detection in the absence of a sequenced genome. We use it to comprehensively identify editing sites in the squid giant axon system and other areas of the nervous system. Surprisingly, almost 60% of all mRNAs studied harbor recoding events, and most at multiple sites. These data show orders of magnitude more recoding in the squid proteome than in any other species studied to date. In squid, editing is so pervasive that the central dogma should be modified to include this process. Our results open the possibility that extensive recoding is common in many organisms, rivaling alternative splicing as a means of creating functional diversity.

Results and discussion

To detect RNA editing sites in the squid nervous system, we generated millions of RNA and genomic DNA reads from an individual squid. Our method differed from previous approaches by using a de novo transcriptome as the point of reference instead of a genome (Figure 1A). The transcriptome was assembled from RNA-seq reads, and each nucleotide within it represents the consensus of many reads. If the majority of RNA reads were edited (‘strong’ editing sites), the transcriptome would differ from the genomic DNA and read ‘G’ where gDNA reads would show ‘A’ (the sequencing process identifies inosines as guanosines). We detected such sites by aligning DNA-seq reads to the transcriptome (Figure 1B). At positions where editing occurred in the minority of RNA-seq reads (‘weak’ editing sites), however, the transcriptome and the genomic DNA would be identical. These sites were detected by identifying variability in RNA-seq, but not DNA-seq, reads (Figure 1B). This general approach is applicable to all organisms that lack a sequenced genome.